Molecular dynamics simulations of mixed DOPC–β-sitosterol bilayers and their interactions with DMSO

ell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulphoxide (DMSO) commonly used in cryopreservation. The interaction of DMSO with model bilayers consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and ß-sitosterol has been studied using molecular dynamics simulations. Initially the effect of sterol concentration and temperature upon bilayers solvated in pure water was determined, and membranes containing ß-sitosterol were compared with membranes containing cholesterol. These simulations showed that the presence of sterols has a condensing effect on the phospholipids, causing a reduction in the area per lipid as the sterol concentration increases, up to a phospholipid–sterol ratio of 2[thin space (1/6-em)]:[thin space (1/6-em)]1. The incorporation of sterols into the bilayer also increased the thickness and order of the phospholipid acyl tails. DOPC–ß-sitosterol bilayers at different relative concentrations were simulated in solutions of 2.5 and 25.0 mol% DMSO. The interaction of DMSO with the bilayers caused the bilayers to expand laterally, while thinning normal to the plane of the bilayer expansion. The same qualitative behaviour has been shown to occur in pure phosphocholine bilayers. However, the presence of sterols made the membranes more resistant to the effects of DMSO, to the extent that the membranes where able to maintain their integrity in 25.0 mol% DMSO, a concentration that would otherwise cause the destruction of a pure DOPC bilayer. Increasing the concentration of ß-sitosterol within the bilayers reduced the rate of DMSO diffusion across the bilayer and, if the concentration was large enough, caused the diffusion mechanism to change. DMSO was observed to disorder the membranes enough to cause an increase in the number of sterol “flip–flops”. The findings of this work provide a more realistic description of how DMSO interacts with cell membranes and the role of the composition of the membrane

What determines sub-diffusive behavior in crowded protein solutions?

This work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk), access to which was provided by the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (https://www.hecbiosim.ac.uk/), supported by EPSRC (grant no. EP/R029407/1). Analysis and visualization of the simulation data were conducted at the Pawsey Supercomputing Centre, therefore this work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia, as well as resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. V.K. gratefully acknowledges the receipt of a scholarship under the Aberdeen-Curtin Alliance collaborative PhD program.Peer reviewedPostprin

Definition Of The Minimal Contents For The Molecular Simulation Of The Yeast Cytoplasm

Funding VK gratefully acknowledges the receipt of a scholarship under the Aberdeen-Curtin Alliance collaborative Ph.D. program. Acknowledgments We thank Prof. Grant Brown (University of Toronto) for making the yeast proteomics datasets available to us.Peer reviewedPublisher PD

Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter

© 2020 The Author(s) The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transporter with the highest quality using the X-ray crystal structure of mouse ABCB1 (Pgp1), a close homologue of ABCB5 and a well-studied member of the ABC family. Molecular dynamics simulations were used to validate the atomistic model of ABCB5 and characterise its structural properties in model cell membranes. Molecular docking simulations of known ABCB5 substrates such as taxanes, anthracyclines, camptothecin and etoposide were then used to identify at least three putative binding sites for chemotherapeutic drugs transported by ABCB5. The location of these three binding sites is predicted to overlap with the corresponding binding sites in Pgp1. These findings will serve as the basis for future in vitro studies to validate the nature of the identified substrate-binding sites in the full-length ABCB5 transporter

The effect of tightly-bound water molecules on scaffold diversity in computer-aided de novo ligand design of CDK2 inhibitors

We have determined the effects that tightly bound water molecules have on the de novo design of cyclin-dependent kinase-2 (CDK2) ligands. In particular, we have analyzed the impact of a specific structural water molecule on the chemical diversity and binding mode of ligands generated through a de novo structure-based ligand generation method in the binding site of CDK2. The tightly bound water molecule modifies the size and shape of the binding site and we have found that it also imposed constraints on the observed binding modes of the generated ligands. This in turn had the indirect effect of reducing the chemical diversity of the underlying molecular scaffolds that were able to bind to the enzyme satisfactorily

A Comparative Structural Bioinformatics Analysis of the Insulin Receptor Family Ectodomain Based on Phylogenetic Information

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight ‘twist’ rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals

Redundancy and the Evolution of Cis-Regulatory Element Multiplicity

The promoter regions of many genes contain multiple binding sites for the same transcription factor (TF). One possibility is that this multiplicity evolved through transitional forms showing redundant cis-regulation. To evaluate this hypothesis, we must disentangle the relative contributions of different evolutionary mechanisms to the evolution of binding site multiplicity. Here, we attempt to do this using a model of binding site evolution. Our model considers binding sequences and their interactions with TFs explicitly, and allows us to cast the evolution of gene networks into a neutral network framework. We then test some of the model's predictions using data from yeast. Analysis of the model suggested three candidate nonadaptive processes favoring the evolution of cis-regulatory element redundancy and multiplicity: neutral evolution in long promoters, recombination and TF promiscuity. We find that recombination rate is positively associated with binding site multiplicity in yeast. Our model also indicated that weak direct selection for multiplicity (partial redundancy) can play a major role in organisms with large populations. Our data suggest that selection for changes in gene expression level may have contributed to the evolution of multiple binding sites in yeast. We conclude that the evolution of cis-regulatory element redundancy and multiplicity is impacted by many aspects of the biology of an organism: both adaptive and nonadaptive processes, both changes in cis to binding sites and in trans to the TFs that interact with them, both the functional setting of the promoter and the population genetic context of the individuals carrying them

Erratum:Heparin/heparan sulphate-based drugs

Published in Drug Discovery Today, 2010, 15(23-24), pp. 1058-1069, DOI: 10.1016/j.drudis.2010.10.009</i

A Simple but Effective Combination of pH Indicators for Plant Tissue Culture

The use of pH indicators provides a simple, semi-quantitative visual method for quickly assessing pH changes in tissue culture media; however, pH indicators are rarely used in routine plant tissue culture media. In this study, chlorophenol red, bromocresol purple, and bromocresol green were tested to assess their functionality in the growth medium for plant shoot cultures. In addition, a combination of bromocresol green and bromocresol purple was tested to determine if they would widen the observable colour change to better assess pH changes in the medium. Varying the ratio of bromocresol green to bromocresol purple alters the pH at which the colour changes from blue to green to yellow, with a 1:3 ratio providing a useful pH range of 5&ndash;6.5, while a 1:1 ratio provides a useful pH range of 4.5&ndash;6. All the pH indicators showed no toxic side effects for the plant species tested in this study and were able to be autoclaved to ensure media sterility. The addition of these pH indicators to quickly assess media pH in large tissue culture collections can aid in routine maintenance. These pH indicators can be used as a &lsquo;traffic light&rsquo; system, with blue indicating a high pH, green a normal pH, and yellow a low pH in the media